Snake was put in prefectly fine. They used the younger, less serious version of him luckilly (not the MGS4 PS3 version), made his guns not so rigged (hes kind enough to RPG the ground) and gave him some cool moves. The music he brought with him was also decent.
Mind you he belongs more in such a game than pokemon do, especially that annoying lucario. Pokemon are weak as hell, they do not even kill each other as apposed to vilans like gannondorf who would stop at nothing to take over the world, samus who has killes 100s of things, and the mass murders of mario and link who have been made famous for killing basdies with the AI of near nothing.
Thus as long as there are big name characters in it (like samus) then snake is perfecly in place (as long as they do not go over the top). Adding someone like master chief on the other hand would be different.
Honestly if you want a game with friendly characters, play pokemon.